Download Multiple global radiations in tadpole shrimps challenge the

Multiple global radiations in tadpole
shrimps challenge the concept of ‘living
fossils’
Thomas C. Mathers1 , Robert L. Hammond2 , Ronald A. Jenner3 ,
Bernd Hänfling1 and Africa Gómez1
1 School of Biological, Biomedical and Environmental Sciences, University of Hull, Hull, UK
2 Department of Biology, University of Leicester, Leicester, UK
3 Life Sciences Department, The Natural History Museum, London, UK
ABSTRACT
‘Living fossils’, a phrase first coined by Darwin, are defined as species with limited
recent diversification and high morphological stasis over long periods of evolutionary time. Morphological stasis, however, can potentially lead to diversification
rates being underestimated. Notostraca, or tadpole shrimps, is an ancient, globally
distributed order of branchiopod crustaceans regarded as ‘living fossils’ because their
rich fossil record dates back to the early Devonian and their morphology is highly
conserved. Recent phylogenetic reconstructions have shown a strong biogeographic
signal, suggesting diversification due to continental breakup, and widespread cryptic
speciation. However, morphological conservatism makes it difficult to place fossil
taxa in a phylogenetic context. Here we reveal for the first time the timing and tempo
of tadpole shrimp diversification by inferring a robust multilocus phylogeny of Branchiopoda and applying Bayesian divergence dating techniques using reliable fossil
calibrations external to Notostraca. Our results suggest at least two bouts of global
radiation in Notostraca, one of them recent, so questioning the validity of the ‘living
fossils’ concept in groups where cryptic speciation is widespread.
Submitted 20 February 2013
Accepted 14 March 2013
Published 2 April 2013
Corresponding author
Africa Gómez, [email protected]
Academic editor
Keith Crandall
Additional Information and
Declarations can be found on
page 8
DOI 10.7717/peerj.62
Copyright
2013 Mathers et al.
Distributed under
Creative Commons CC-BY 3.0
OPEN ACCESS
Subjects Evolutionary Studies
Keywords Triops, Notostraca, Lepidurus, Biogeography, Diversification, Fossil, Bayesian analysis,
‘Living fossil’, Divergence time
INTRODUCTION
There has been much debate about the tempo and mode of the diversification of life
(Eldredge & Gould, 1972; Reznick & Ricklefs, 2009; Rhodes, 1983). Recently, this debate
has been informed by dating using relaxed molecular clocks and diversification analyses;
techniques which have revealed disparate patterns of speciation with early bursts (Burbrink
& Pyron, 2010), recent radiations (Nagalingum et al., 2011) and density dependency
(Phillimore & Price, 2008) being demonstrated. One extreme and often controversial
pattern of diversification is found in ‘living fossils’, a concept introduced by Charles
Darwin in On the Origin of Species when dealing with the perplexing nature of the platypus
and lungfish, relicts of once diverse groups (Darwin, 1859). Since Darwin’s first use, the
‘living fossil’ term has been applied to groups which appear to have diversified little and are
morphologically stable over long periods of evolutionary time, with examples including
How to cite this article Mathers et al. (2013), Multiple global radiations in tadpole shrimps challenge the concept of ‘living fossils’. PeerJ
1:e62; DOI 10.7717/peerj.62
cycads, tuatara, coelacanths, horseshoe crabs and Ginkgo biloba. However, morphological
stasis can obscure the patterns of species diversification, and recent time-calibrated
phylogenetic analyses of some ‘living fossils’ have indeed revealed that extant species are in
fact only recently diverged (Kano et al., 2012; Nagalingum et al., 2011).
Notostraca, or tadpole shrimps, is an ancient, globally distributed order of branchiopod
crustaceans with a rich fossil record dating back to the early Devonian (Fayers & Trewin,
2002). The order has two extant genera, Triops and Lepidurus, in the family Triopsidae,
with a yet undefined number of species. The nomenclature and systematic position
of some ancient extinct Notostraca lineages, is, however, problematic (Hegna & Dong,
2010). This is partly because tadpole shrimps have maintained an extremely conserved,
yet complex, bauplan with extant species indistinguishable from fossils of Triops from the
Triassic (Gall & Grauvogel-Stamm, 2005; Gore, 1986; Trusheim, 1938) and of Lepidurus in
the Jurassic (Barnard, 1929; Haughton, 1924). This striking morphological conservatism
has led them to be referred to as ‘living fossils’ (Fryer, 1988; King & Hanner, 1998;
Mantovani et al., 2008).
Phylogenetic reconstructions of extant Notostraca show a strong biogeographic signal
(Mathers et al., 2013; Vanschoenwinkel et al., 2012). In Triops, species complexes are largely
restricted to single continents, while Lepidurus lineages show high levels of endemism
(Rogers, 2001), patterns that suggest ancient radiation with diversification through
continental break-up. However, the extreme morphological conservatism of this order
hampers both the taxonomy of extant species and the phylogenetic placement of fossil
taxa, with little known about the timing and tempo of notostracan diversification. Genetic
analyses have revealed widespread cryptic species (King & Hanner, 1998; Korn et al., 2010;
Korn & Hundsdoerfer, 2006; Macdonald, Sallenave & Cowley, 2011; Vanschoenwinkel et al.,
2012), further illustrating the difficulty of inferring past and present diversity. To address
this difficulty we infer a robust phylogeny of all known notostracan species from both
extant genera and seven branchiopod outgroups. Our analysis uses all available Notostraca
sequence data for seven genes, and Bayesian relaxed clock dating techniques, with multiple
branchiopod fossil calibrations, to estimate divergence times.
MATERIALS AND METHODS
Species delimitation
As Notostraca is known to contain cryptic species complexes (e.g. King & Hanner, 1998),
and in order to follow the same criterion for species selection for the multilocus analysis,
we delimited species using a generalised mixed Yule coalescent (GMYC) model (Pons et al.,
2006) fitted to an ultrametric phylogeny based on all available cytochrome oxidase I (COI)
sequences from GenBank. The 270 sequences were aligned with Muscle (Edgar, 2004) and
phylogeny estimated with BEAST v1.7.4 (Drummond et al., 2012) under a constant population size coalescent tree model and GTR +0 substitution model. A strict molecular clock
was used with the substitution rate fixed to 1 to provide branch lengths relative to an arbitrary time scale. The MCMC chain was run for 9,000,000 iterations with the first 500,000
iterations removed as burnin. Effective sample sizes (ESS’s) of parameters (all greater
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
2/12
than 200) and appropriate burnin were checked using Tracer v1.5 (Rambaut & Drummond,
2007). From this a maximum clade credibility tree using median heights was made.
We then fitted a single threshold GMYC model to the COI tree to delimit species from
populations. A total of 34 species of Notostraca were identified in this analysis (Table S1).
Multilocus phylogenetic analysis of Branchiopoda
We constructed a multilocus alignment containing representatives of all known species
of Notostraca. Single representatives of each phylogenetic species identified by the
GMYC analysis were selected for inclusion in our phylogenetic analysis. In addition,
four Notostraca lineages (T. gadensis, T. cf. granarius Tunisia, L. bilobatus and L. cryptus),
which did not have COI data available, but were represented by other genes, were also
used in our multilocus phylogenetic analysis. The species status of these lineages has been
confirmed in regional studies of cryptic diversity (King & Hanner, 1998; Korn et al., 2010;
Korn & Hundsdoerfer, 2006; Rogers, 2001). We also included seven representatives of the
other branchiopod orders so that robust fossil calibrations could be applied for the dating
analysis. We included sequences for the genes 12S, 16S, 28S, cytochrome oxidase I (COI),
Elongation Factor 1-alpha (EF1), RNA Polymerase II and Glycogen Synthase (see Table S2
for Accession Numbers).
Sequences were aligned using MUSCLE (Edgar, 2004) with final adjustments by
eye. Introns in the nuclear protein coding genes were identified and removed based
on alignment with available Notostraca mRNAs. Translation was checked in MEGA 5
(Tamura et al., 2011). Overall, sequences for 45 taxa (38 notostracan and 7 branchiopod
outgroups) were concatenated for analysis with the alignment containing 5793 positions
and 52% missing data (Table S2; the alignment file is available in Dryad DOI 10.5061/
dryad.77bt2).
Optimum partitioning schemes and substitution models for our phylogenetic analysis
and divergence time estimation were identified using PartitionFinder (Lanfear et al., 2012).
PartitionFinder uses a heuristic search algorithm, starting with a fully partitioned analysis
(gene and codon position where appropriate), and identifies the best fit partitioning
scheme and substitution models based on Bayesian Information Criterion (BIC). Due to
the restricted model choice available in RAxML (Stamatakis, 2006) we conducted separate
PartitionFinder analyses for the phylogenetic analysis and divergence time estimation.
For the phylogenetic analysis we restricted model choice options to GTR or GTR +0,
whereas for divergence time estimation we allowed models to be selected from the full
suite available in BEAST. We excluded models with proportion of invariant sites (+I)
as rate heterogeneity is accounted for by the gamma shape parameter (+0). Optimum
partitioning schemes and substitution models for both analyses are given in Tables S3
and S4.
Branchiopod phylogeny was estimated using Bayesian and maximum likelihood (ML)
methods with partitions and substitution models set to those identified by PartitionFinder
(Table S3). Bayesian analysis was performed with MrBayes v3.2 (Ronquist et al., 2012).
Model parameters between partitions were unlinked. Two independent MCMC chains
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
3/12
Table 1 Fossils used to calibrate divergence time analysis in BEAST. Age constraints are treated as hard bounds unless otherwise stated. Node
numbers indicate phylogenetic placement of fossil calibrations in Fig. 1.
Node
Fossil taxa
Geological period
Minimum age
(Mya)
Maximum age
(Mya)
Reference
1
Oldest Bilateria eg. Kimberella
Ediacaran
-
558
1
1
Rehbachiella
Undescribed anostracan
Upper Cambrian
Base Ordovician
488
500 (soft max)
-
2
3
4
Castracollis
Ebullitiocaris elatus
Daphnia and Ctenodaphnia sp.
Pragian, Early Devonian
Carboniferous
Jurassic/Cretaceous
410
300
145
-
Fedonkin, Simonetta &
Ivantsov (2007)
Waloßek (1995)
Harvey, Vélez &
Butterfield (2012)
Fayers & Trewin (2002)
Womack et al. (2012)
Kotov & Taylor (2011)
were run for 10,000,000 iterations each, sampling every 5,000 iterations. The first 25%
of each run was discarded as burnin with the remaining samples pooled and used to
create a maximum clade credibility tree. Maximum likelihood phylogenetic analysis was
performed using RAxMLHPC-PTHREADS v7.0.4 (Stamatakis, 2006). An initial ML search
using GTR + 04 was performed onto which 100 rapid bootstraps were drawn.
Bayesian relaxed clock divergence dating
We estimated Bayesian divergence times with BEAST v1.7.4 (Drummond et al., 2012) using
an uncorrelated lognormal relaxed clock (Drummond et al., 2006) and a Yule speciation
prior. XML files for all BEAST runs were created using BEAUTi v1.7.4 (Drummond
et al., 2012). Topology was constrained to that of the unconstrained RAxML analysis.
We used the best fit partitioning scheme identified by PartitionFinder (Table S4) and
estimated substitution model parameters independently for each partition. Initial runs
were conducted using substitution models identified by PartitionFinder, however, this
resulted in poor mixing of some GTR model parameters for partitions 1, 2 and 5, so
subsequent runs were performed using a simpler HKY +0 model for these partitions.
Five branchiopod fossils representing the oldest known occurrences of their respective
crown groups were used to calibrate the molecular clock with minimum age constraints
(Table 1). Lognormal prior distributions were used to specify the level of uncertainty in
the placement of these fossil calibrations as they reflect the likely scenario that the true date
of divergence of a given node was some time before the earliest known fossil belonging
to that clade (Ho & Phillips, 2009). Lognormal distributions have three parameters –
mean, standard deviation and offset. We set the offset to correspond to the minimum
age of the node as determined by the fossil record, we then specified mean and standard
deviations that resulted in 95% of the distribution falling between the age of the fossil
and the age of the next oldest fossil (at a lower taxonomic level) for that group. This gives
a prior distribution, which assigns the majority of the probability close to the age of the
oldest known fossil, but gives a long tail to account for uncertainty in the proximity of
the fossil to the true date of divergence. As Bayesian divergence dating benefits from at
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
4/12
least one maximum age constraint we conservatively constrained the root of the tree to a
maximum age of 558 Mya, the age of the oldest bilaterian fossil (Fedonkin, Simonetta &
Ivantsov, 2007).
We ran two independent BEAST MCMC chains for 50,000,000 iterations, sampling
every 5000 iterations. Ten million iterations were removed as burnin from each run.
Convergence of the two runs and the ESS of parameter estimates (all greater than
250) where assessed using Tracer v1.5 (http://tree.bio.ed.ac.uk/software/tracer/). A
posterior sample of 8000 trees from one of the runs was used to construct a maximum
clade credibility time tree for Notostraca and our selected outgroups. The XML file
used to run the BEAST divergence time analysis can be downloaded from Dryad
DOI 10.5061/dryad.77bt2.
Diversification analysis
Patterns of diversification through time within Notostraca were investigated using LASER
(Rabosky, 2006) based on the BEAST time tree with outgroups pruned. Using LASER we
compared constant rate and variable rate speciation models using likelihood ratio tests
(Table S5).
RESULTS AND DISCUSSION
The most complete taxon sampling to date coupled with the inclusion of multiple nuclear
and mitochondrial markers allowed us to generate a robust phylogeny of 38 extant
Notostraca species. ML and Bayesian inference gave highly congruent phylogenetic trees
with most branches highly supported (Figs. S1 and S2). The recovered relationships
between branchiopod orders are in agreement with recently published arthropod
phylogenies (Regier et al., 2010; von Reumont et al., 2012), providing a solid platform
for divergence dating analysis.
Our robust time-calibrated phylogeny of Branchiopoda (Fig. 1) clearly shows that
Notostraca has a pattern of diversity incompatible with Darwin’s original usage of the term
‘living fossil’ as relics of once diverse groups, and importantly reveals cryptic patterns of
diversification. Our analysis – using outgroup fossil calibrations – estimates an ancient
divergence of Triops and Lepidurus during the Jurassic, 184 Mya (95% confidence interval
132–259 Mya), which agrees with the earliest fossils assigned to Lepidurus (Barnard, 1929;
Gand, Garric & Lapeyrie, 1997), and with a sister relationship of Notostraca to the extinct
order Kazacharthra of the Late Triassic/Early Jurassic (Olesen, 2009). This initial radiation
of extant Notostraca was not, however, due to continental break up as the timing and
pattern of diversification within the genera substantially postdates the break-up of Pangaea
160–138 Mya (Scotese, 2001). Furthermore, the current species distributions of Triops and
Lepidurus are likely to have resulted from a second global radiation of the order, possibly
following considerable levels of extinction. We conclude this because fossil Notostraca,
attributed to Triops and Lepidurus, have been found in modern day North and South
America, Europe, Africa and Antarctica, implying a global distribution by the early Jurassic
(Gall & Grauvogel-Stamm, 2005; Gand, Garric & Lapeyrie, 1997; Garrouste, Nel & Gand,
2009; Gore, 1986; Haughton, 1924; Trusheim, 1938). Yet, our LASER analysis shows a
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
5/12
Figure 1 Time calibrated phylogeny of 38 notostracan species and seven branchiopod outgroups. Numbers at nodes correspond to the fossil
calibrations given in Table 1. Nodes with black circles have ML Bootstrap support values greater than 70 and posterior probabilities greater than 95
from the RAxML and MrBayes analyses respectively. Error bars show the 95% confidence intervals of divergence times. Colour coded squares show
the known geographic distribution of each species.
significant increase in the rate of diversification of Notostraca about 73 Mya (Fig. 2),
close to the time of the K-Pg mass extinction event. It is this second radiation that resulted
in the current global distribution of extant Triops and Lepidurus.
The almost synchronous radiation of Triops and Lepidurus (Fig. 1) suggests that a
common factor may have triggered diversification of the two genera. The diversification
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
6/12
Figure 2 Diversification of Notostraca through time. Arrows indicate the timing and direction of
shifts in rate of diversification inferred by LASER. N is the number of species. The best fit ML model
of diversification identified three distinct rates of diversification during the evolutionary history of
Notostraca with an increase in speciation rate 73 Mya followed by a decrease 6 Mya.
of modern birds – widely involved in dispersal in aquatic invertebrates (Green et al., 2005;
van Leeuwen et al., 2012) – coincided with the initiation of the notostracan radiation
(Pacheco et al., 2011), and may have facilitated the long distance dispersal and subsequent
diversification of Notostraca. Indeed, the geographical distribution of extant taxa (Fig. 1)
suggests several instances of intercontinental dispersal. For example, the colonisation
of North America from Australia could have resulted from dispersal events during bird
migration. Such long distance dispersal and colonisation events might also have been
facilitated by the flexible nature of sexual systems found within Notostraca (Mathers
et al., 2013). Indeed, the evolution of androdioecy – a sexual system where males and
hermaphrodites coexist (Weeks, 2012; Zierold, Hanfling & Gómez, 2007; Zierold et al.,
2009) – from gonochorism appears to have favoured postglacial recolonisation in the
species Triops cancriformis (Zierold, Hanfling & Gómez, 2007) and in Notostraca as a whole
(Mathers et al., 2013).
The concept of ‘living fossils’ has been a controversial one as it has often been
interpreted to imply a lack of evolutionary change, even against evidence of molecular
evolutionary change (Avise, Nelson & Sugita, 1994; Casane & Laurenti, 2013). Our
divergence dating analysis has shown that tadpole shrimps can be regarded as ‘living
fossils’ only on the grounds of morphological conservatism, not on the basis of limited
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
7/12
diversification or relict status. Instead, throughout their long evolutionary history,
notostracans have undergone multiple global radiations and high species turnover. Recent,
time calibrated, phylogenetic analysis of other traditional ‘living fossils’ such as cycads
(Nagalingum et al., 2011), nautiloids (Wray et al., 1995), horseshoe crabs (Obst et al.,
2012) and monoplacophorans (Kano et al., 2012), have also revealed that extant species are
more recently diverged than suggested by fossil data alone. We therefore caution against
drawing conclusions about patterns of diversification based on fossil data alone in groups
where widespread morphological conservatism may obscure rampant cryptic speciation.
Furthermore, our results help clarify the term ‘living fossils’, putting important questions
into focus. Namely, is such morphological conservatism, in the face of evolutionarily
recent diversification and radiation, best accounted for by unchanging selection or by
developmental genetic constraints?
ACKNOWLEDGEMENTS
This work was part of TCM’s Ph.D. We thank Chris Venditti for his help with the analyses,
and Dave Lunt and Steve Moss for bioinformatics support. Domino Joyce read and
provided constructive comments in a previous version of the manuscript.
ADDITIONAL INFORMATION AND DECLARATIONS
Funding
This work was part of TCM’s Ph.D., funded by a NERC CASE Studentship NE/G012318/1.
AG was supported by a NERC Advanced fellowship NE/B501298/1.The funders had no
role in study design, data collection and analysis, decision to publish, or preparation of the
manuscript.
Grant Disclosures
The following grant information was disclosed by the authors:
NERC CASE Studentship: NE/G012318/1.
NERC Advanced fellowship: NE/B501298/1.
Competing Interests
There are no Competing Interests to declare.
Author Contributions
• Thomas C. Mathers conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper.
• Robert L. Hammond, Ronald A. Jenner, Bernd Hänfling and Africa Gómez conceived
and designed the experiments, wrote the paper.
Data Deposition
The following information was supplied regarding the deposition of related data:
Dryad: DOI 10.5061/dryad.77bt2
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
8/12
Supplemental Information
Supplemental information for this article can be found online at http://dx.doi.org/
10.7717/peerj.62.
REFERENCES
Avise JC, Nelson WS, Sugita H. 1994. A speciational history of “living fossils”: molecular
evolutionary patterns in horseshoe crabs. Evolution 48:1986–2001 DOI ./.
Barnard KH. 1929. A revision of the South African Branchiopoda Phyllopoda. Annals of the South
African Museum 29:181–272.
Burbrink FT, Pyron RA. 2010. How does ecological opportunity influence rates of speciation,
extinction, and morphological fiversification in New World ratsnakes (tribe Lampropeltini)?
Evolution 64:934–943 DOI ./j.-...x.
Casane D, Laurenti P. 2013. Why coelacanths are not ‘living fossils’. BioEssays 35(4):332–338
DOI ./bies..
Darwin C. 1859. On the origin of species by means of natural selection. London: Murray.
Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with
confidence. PLoS Biology 4:e88 DOI ./journal.pbio..
Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and
the BEAST 1.7. Molecular Biology and Evolution 29:1969–1973 DOI ./molbev/mss.
Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic Acids Research 32:1792–1797 DOI ./nar/gkh.
Eldredge N, Gould SJ. 1972. Punctuated equilibria: an alternative to phyletic gradualism. Models
in Paleobiology 82–115.
Fayers SR, Trewin NH. 2002. A new crustacean from the Early Devonian Rhynie chert,
Aberdeenshire, Scotland. Earth and Environmental Science Transactions of the Royal Society of
Edinburgh 93:355–382 DOI ./SX.
Fedonkin MA, Simonetta A, Ivantsov AY. 2007. New data on Kimberella, the Vendian mollusc-like
organism (White Sea region, Russia): palaeoecological and evolutionary implications. London:
Geological Society 286:157–179. Special Publications.
Fryer G. 1988. Studies on the functional-morphology and biology of the Notostraca (Crustacea,
Branchiopoda). Philosophical Transactions of the Royal Society of London Series B-Biological
Sciences 321:27–142 DOI ./rstb...
Gall J-C, Grauvogel-Stamm L. 2005. The early middle Triassic ‘Grès à Voltzia’ formation of
eastern France: a model of environmental refugium. Comptes Rendus Palevol 4:637–652
DOI ./j.crpv....
Gand G, Garric J, Lapeyrie J. 1997. Biocénoses à triopsidés (Crustacea, Branchiopoda) du Permien
du bassin de Lodève (France). Geobios 30:673–700 DOI ./S-()-X.
Garrouste R, Nel A, Gand G. 2009. New fossil arthropods (Notostraca and Insecta:
Syntonopterida) in the continental Middle Permian of Provence (Bas-Argens Basin, France).
Comptes Rendus Palevol 8:49–57 DOI ./j.crpv....
Gore PJW. 1986. Triassic notostracans in the Newark supergroup, Culpeper Basin, Northern
Virginia. Journal of Paleontology 60:1086–1096.
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
9/12
Green AJ, Sánchez MI, Amat F, Figuerola J, Hontoria F, Ruiz O, Hortas F. 2005. Dispersal
of invasive and native brine shrimps Artemia (Anostraca) via waterbirds. Limnology and
Oceanography 50:737–742 DOI ./lo.....
Harvey THP, Vélez MI, Butterfield NJ. 2012. Exceptionally preserved crustaceans from western
Canada reveal a cryptic Cambrian radiation. Proceedings of the National Academy of Sciences
109:1589–1594 DOI ./pnas..
Haughton S. 1924. The fauna and stratigraphy of the Stormberg series. Annals of the South African
Museum 12:323–497.
Hegna TA, Dong REN. 2010. Two new “Notostracans”, Chenops gen. nov. and Jeholops gen.
nov.(Crustacea: Branchiopoda:? Notostraca) from the Yixian Formation, northeastern China.
Acta Geologica Sinica 84:886–894 (English Edition) DOI ./j.-...x.
Ho SYW, Phillips MJ. 2009. Accounting for calibration uncertainty in phylogenetic estimation of
evolutionary divergence times. Systematic Biology 58:367–380 DOI ./sysbio/syp.
Kano Y, Kimura S, Kimura T, Warén A. 2012. Living Monoplacophora: morphological
conservatism or recent diversification? Zoologica Scripta 41:471–488 DOI ./j....x.
King JL, Hanner R. 1998. Cryptic species in a “living fossil” lineage: taxonomic and phylogenetic
relationships within the genus Lepidurus (Crustacea: Notostraca) in North America. Molecular
Phylogenetics and Evolution 10:23–36 DOI ./mpev...
Korn M, Green AJ, Machado M, Garcia-de-Lomas J, Cristo M, da Fonseca LC, Frisch D,
Perez-Bote JL, Hundsdoerfer AK. 2010. Phylogeny, molecular ecology and taxonomy of
southern Iberian lineages of Triops mauritanicus (Crustacea: Notostraca). Organisms Diversity
and Evolution 10:409–440 DOI ./s---y.
Korn M, Hundsdoerfer AK. 2006. Evidence for cryptic species in the tadpole shrimp Triops
granarius (Lucas, 1864) (Crustacea: Notostraca). Zootaxa 1257:57–68.
Kotov AA, Taylor DJ. 2011. Mesozoic fossils (>145 Mya) suggest the antiquity of the subgenera
of Daphnia and their coevolution with chaoborid predators. BMC Evolutionary Biology 11:129
DOI ./---.
Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. Partitionfinder: combined selection of
partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology
and Evolution 29:1695–1701 DOI ./molbev/mss.
Macdonald KS, Sallenave R, Cowley DE. 2011. Morphological and genetic variation in Triops
(Branchiopoda: Notostraca) from ephemeral waters of the northern Chihuahuan desert of
North America. Journal of Crustacean Biology 31:468–484 DOI ./-..
Mantovani B, Cesari M, Luchetti A, Scanabissi F. 2008. Mitochondrial and nuclear DNA
variability in the living fossil Triops cancriformis (Bosc, 1801) (Crustacea, Branchiopoda,
Notostraca). Heredity 100:496–505 DOI ./hdy...
Mathers TC, Hammond RL, Jenner RA, Zierold T, Hänfling B, Gómez A. 2013. High lability of
sexual system over 250 million years of evolution in morphologically conservative tadpole
shrimps. BMC Evolutionary Biology 13:30 DOI ./---.
Nagalingum NS, Marshall CR, Quental TB, Rai HS, Little DP, Mathews S. 2011. Recent
synchronous radiation of a living fossil. Science 334:796–799 DOI ./science..
Obst M, Faurby S, Bussarawit S, Funch P. 2012. Molecular phylogeny of extant horseshoe
crabs (Xiphosura, Limulidae) indicates Paleogene diversification of Asian species. Molecular
Phylogenetics and Evolution 62:21–26 DOI ./j.ympev....
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
10/12
Olesen J. 2009. Phylogeny of Branchiopoda (Crustacea)—character evolution and contribution of
uniquely preserved fossils. Arthropod Systematics and Phylogeny 67:3–39.
Pacheco MA, Battistuzzi FU, Lentino M, Aguilar R, Kumar S, Escalante AA. 2011. Evolution of
modern birds revealed by mitogenomics: timing the radiation and origin of major orders.
Molecular Biology and Evolution 28:1927–1942 DOI ./molbev/msr.
Phillimore AB, Price TD. 2008. Density-dependent cladogenesis in birds. PLoS Biology 6:e71
DOI ./journal.pbio..
Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S,
Sumlin WD, Vogler AP. 2006. Sequence-based species delimitation for the DNA taxonomy
of undescribed insects. Systematic Biology 55:595–609 DOI ./.
Rabosky DL. 2006. LASER: a maximum likelihood toolkit for detecting temporal shifts in
diversification rates from molecular phylogenies. Evolutionary Bioinformatics Online 2:
273–276.
Rambaut A, Drummond A. 2007. Tracer v1.4 [updated to v1.5]
Available at http://beast.bio.ed.ed.ac.uk/Tracer.
Regier JC, Shultz JW, Zwick A, Hussey A, Ball B, Wetzer R, Martin JW, Cunningham CW.
2010. Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding
sequences. Nature 463:1079–1083 DOI ./nature.
Reznick DN, Ricklefs RE. 2009. Darwin’s bridge between microevolution and macroevolution.
Nature 457:837–842 DOI ./nature.
Rhodes FHT. 1983. Gradualism, punctuated equilibrium and the origin of species. Nature
305:269–272 DOI ./a.
Rogers DC. 2001. Revision of the nearctic Lepidurus (Notostraca). Journal of Crustacean Biology
21:991–1006 DOI ./-()[:ROTNLN]..CO;.
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L,
Suchard MA, Huelsenbeck JP. 2012. MrBayes 3.2: efficient Bayesian phylogenetic
inference and model choice across a large model space. Systematic Biology 61:539–542
DOI ./sysbio/sys.
Scotese CR. 2001. Atlas of earth history: University of Texas at Arlington. Department of Geology.
PALEOMAP Project.
Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic
analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690
DOI ./bioinformatics/btl.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular
evolutionary genetics analysis using maximum likelihood, evolutionary distance,
and maximum parsimony methods. Molecular Biology and Evolution 28:2731–2739
DOI ./molbev/msr.
Trusheim F. 1938. Triopsiden (Crust. Phyll.) aus dem Keuper Frankens. Paläontologische Zeitschrift
19:198–216.
van Leeuwen CHA, van der Velde G, van Groenendael JM, Klaassen M. 2012. Gut travellers:
internal dispersal of aquatic organisms by waterfowl. Journal of Biogeography 39:2031–2040
DOI ./jbi..
Vanschoenwinkel B, Pinceel T, Vanhove MPM, Denis C, Jocque M, Timms BV, Brendonck L.
2012. Toward a global phylogeny of the “living fossil” crustacean order of the Notostraca. PLoS
ONE 7:e34998 DOI ./journal.pone..
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
11/12
von Reumont BM, Jenner RA, Wills MA, Dell’Ampio E, Pass G, Ebersberger I, Meyer B,
Koenemann S, Iliffe TM, Stamatakis A, Niehuis O, Meusemann K, Misof B. 2012.
Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia
as the possible sister group of Hexapoda. Molecular Biology and Evolution 29:1031–1045
DOI ./molbev/msr.
Waloßek D. 1995. The Upper Cambrian Rehbachiella, its larval development, morphology
and significance for the phylogeny of Branchiopoda and Crustacea. Hydrobiologia 298:1–13
DOI ./BF.
Weeks SC. 2012. The role of androdioecy and gynodioecy in mediating evolutionary
transitions between dioecy and hermaphroditism in the Animalia. Evolution 66:3670–3686
DOI ./j.-...x.
Womack T, Slater BJ, Stevens LG, Anderson LI, Hilton J. 2012. First cladoceran fossils from
the Carboniferous: palaeoenvironmental and evolutionary implications. Palaeogeography,
Palaeoclimatology, Palaeoecology 344–345:39–48 DOI ./j.palaeo....
Wray CG, Landman NH, Saunders WB, Bonacum J. 1995. Genetic divergence and geographic
diversification in Nautilus. Paleobiology 21:220–228.
Zierold T, Hanfling B, Gómez A. 2007. Recent evolution of alternative reproductive modes in the
‘living fossil’ Triops cancriformis. BMC Evolutionary Biology 7:161 DOI ./---.
Zierold T, Montero-Pau J, Hänfling B, Gómez A. 2009. Sex ratio, reproductive mode
and genetic diversity in Triops cancriformis. Freshwater Biology 54:1392–1405
DOI ./j.-...x.
Mathers et al. (2013), PeerJ, DOI 10.7717/peerj.62
12/12